CYP7A1
Basic information
Region (hg38): 8:58490178-58500163
Previous symbols: [ "CYP7" ]
Links
Phenotypes
GenCC
Source:
- hypercholesterolemia due to cholesterol 7alpha-hydroxylase deficiency (Supportive), mode of inheritance: Semidominant
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP7A1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 23 | 31 | ||||
missense | 91 | 95 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 5 | 3 | 8 | |||
non coding | 13 | 24 | ||||
Total | 1 | 0 | 111 | 38 | 10 |
Highest pathogenic variant AF is 0.0000263
Variants in CYP7A1
This is a list of pathogenic ClinVar variants found in the CYP7A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
8-58491466-G-C | CYP7A1-related disorder | Likely benign (May 10, 2024) | ||
8-58491468-CA-ATT | Uncertain significance (Jul 31, 2018) | |||
8-58491470-T-C | Uncertain significance (Jan 27, 2017) | |||
8-58491517-T-C | Uncertain significance (May 07, 2018) | |||
8-58491521-G-A | Uncertain significance (Jan 15, 2022) | |||
8-58491521-G-C | not specified | Uncertain significance (Nov 22, 2023) | ||
8-58491529-G-A | Likely benign (Jan 12, 2023) | |||
8-58491542-C-T | Uncertain significance (Feb 22, 2022) | |||
8-58491543-G-A | not specified | Uncertain significance (Nov 17, 2022) | ||
8-58491580-T-A | Likely benign (Oct 23, 2023) | |||
8-58491581-A-G | CYP7A1-related disorder | Conflicting classifications of pathogenicity (Mar 16, 2021) | ||
8-58491606-G-C | Uncertain significance (Dec 19, 2022) | |||
8-58491608-A-G | Uncertain significance (May 02, 2017) | |||
8-58491616-C-A | Uncertain significance (Oct 25, 2022) | |||
8-58491633-C-T | Uncertain significance (Aug 10, 2016) | |||
8-58491642-C-T | Uncertain significance (Mar 13, 2023) | |||
8-58491656-G-A | CYP7A1-related disorder | Uncertain significance (Sep 02, 2024) | ||
8-58491686-A-G | not specified | Uncertain significance (May 06, 2024) | ||
8-58491689-T-G | Uncertain significance (Nov 24, 2024) | |||
8-58491697-C-A | not specified | Uncertain significance (Oct 04, 2022) | ||
8-58491698-T-C | CYP7A1-related disorder | Uncertain significance (Mar 25, 2016) | ||
8-58491715-A-G | Likely benign (Feb 26, 2024) | |||
8-58491741-C-T | Uncertain significance (Oct 05, 2023) | |||
8-58491742-G-A | Benign/Likely benign (Nov 22, 2023) | |||
8-58491750-CAA-C | Uncertain significance (Jul 17, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CYP7A1 | protein_coding | protein_coding | ENST00000301645 | 6 | 10059 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000245 | 0.984 | 125698 | 0 | 50 | 125748 | 0.000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.459 | 292 | 271 | 1.08 | 0.0000148 | 3348 |
Missense in Polyphen | 125 | 111.32 | 1.1228 | 1366 | ||
Synonymous | -0.0291 | 105 | 105 | 1.00 | 0.00000626 | 945 |
Loss of Function | 2.13 | 9 | 19.0 | 0.472 | 0.00000100 | 249 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000243 | 0.000242 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.000231 | 0.000231 |
European (Non-Finnish) | 0.000282 | 0.000281 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000163 | 0.000163 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes a rate-limiting step in cholesterol catabolism and bile acid biosynthesis by introducing a hydrophilic moiety at position 7 of cholesterol. Important for cholesterol homeostasis. {ECO:0000269|PubMed:19965590}.;
- Pathway
- Steroid hormone biosynthesis - Homo sapiens (human);Bile secretion - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);Primary bile acid biosynthesis - Homo sapiens (human);PPAR signaling pathway - Homo sapiens (human);Statin Pathway, Pharmacodynamics;27-Hydroxylase Deficiency;Bile Acid Biosynthesis;Congenital Bile Acid Synthesis Defect Type II;Cerebrotendinous Xanthomatosis (CTX);Zellweger Syndrome;Familial Hypercholanemia (FHCA);Congenital Bile Acid Synthesis Defect Type III;Drug Induction of Bile Acid Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Liver X Receptor Pathway;Vitamin D Receptor Pathway;PPAR Alpha Pathway;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Angiopoietin Like Protein 8 Regulatory Pathway;PPAR signaling pathway;Liver steatosis AOP;Oxidation by Cytochrome P450;Statin Pathway;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Endogenous sterols;Cytochrome P450 - arranged by substrate type;Biological oxidations;Metabolism;Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol;Synthesis of bile acids and bile salts via 27-hydroxycholesterol;Synthesis of bile acids and bile salts;Bile acid and bile salt metabolism;Metabolism of steroids;Bile acid biosynthesis;Steroids metabolism;bile acid biosynthesis, neutral pathway
(Consensus)
Recessive Scores
- pRec
- 0.672
Intolerance Scores
- loftool
- 0.730
- rvis_EVS
- 0.09
- rvis_percentile_EVS
- 60.47
Haploinsufficiency Scores
- pHI
- 0.727
- hipred
- N
- hipred_score
- 0.295
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.774
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cyp7a1
- Phenotype
- vision/eye phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- bile acid biosynthetic process;cholesterol catabolic process;sterol metabolic process;regulation of lipid metabolic process;cholesterol homeostasis;positive regulation of cholesterol biosynthetic process;negative regulation of fatty acid biosynthetic process;oxidation-reduction process;regulation of bile acid biosynthetic process;cellular response to glucose stimulus;cellular response to cholesterol
- Cellular component
- endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
- Molecular function
- iron ion binding;cholesterol 7-alpha-monooxygenase activity;heme binding